I have tried both and by far the superior reception is outside. Sorry, that's just how it is. Inside you will reduce signal strength but for your application does it reduce it enough to hurt the navigation?
But I also have mine permanently install inside UNDER my dash.
The antenna needs a metal plate to stick to, not only will it keep it in place but the metal is a ground plane and increases it's ability to pick up sat signals. So if you put it inside the car, make sure you get a good metal plate, I got a 1/16 inch thick steel 3x3 plate and mounted it inside the car and stuck it to the antenna.
I tried on the roof: excellent reception all sats all the time.
I tried inside with just the metal foil they give you: too poor of a signal strength for accurate navigation.
Then I tried putting a thick metal plate below it while inside: and got about 75% of the signal strength. Decent enough for good navigation along with the vss wire.
So I kept it inside with the good piece of metal.
But of course try it where ever you want and see how it works. Check the signal strength and see how good it is in different positions. You can even roll down the window and stick it to the roof for a sec and see how it is up there. Your vehicle might work different than my Aviator and the best thing is to just try different locations and see what works for your vehicle.